Getting a USB PIC to emulate a keyboard is easy-peasy- MicroChip have a project up on their website that does just that, using minimal parts, and it's in assembler, so it's easy to build and program onto a micro. Changing the output from it is not too tough either- I've played with it some, and changing it to output a character or string of characters on a button press is very easy.

Next, throw in AutoHotKey. This is an INSANELY powerful macroing program. It can launch multiple applications and track and send commands to each individual one without bringing them to the foreground. It can do some basic machine vision on the monitor- I used it at one point to trigger a logic analyzer when an image coming out of a camera changed. It's REALLY amazing.

Assign some weirdo keystroke (say, CTRL+ALT+SHIFT+F1) to the action you want to take on the PC through AutoHotKey, then set up the micro to do it. It becomes even easier if the application can run in the foreground- AutoHotKey is very capable of x,y coordinate mouse clicks and menu navigation, so even if the app doesn't have a keystroke shortcut (or series of keystrokes) for what you want to do, you can still work it.

I want turn a MS-20 midi controller into a closer realization of the real thing. I purchased one about a year ago and never use it because it needs to be plugged in to a computer and running windows, there was a mac version but it wasn't Universal Binary that may have changed....

but anyways I would like to control the synth without having to interface with a computer and I was looking into smaller footprint computers and thinking about stuffing one inside the controller and using a uC to control what is going on.

Midi won't work because not all of the values are assignable to midi values. Win Automation will work with hot keys, and I agree with Uptown the keyboard hack with a uC is easy. Hot Key after taking a quick look at it appears to be more capable of customization.

Oh and as an added bonus the MS-20 get 32 voice polyphony instead being monophonic like the original.